Hi Hector,
I'm cc'ing the Bioconductor mailing list. Hope you don't mind.
On 04/04/2014 04:22 PM, Hector Zenil wrote:
> Hi Herv?
>
> I have installed, the latest versions of R and BiConductor and
clite,
> etc. But BSgenome.Hsapiens.NCBI.GRCh38 doesn't come in the available
> genomes. Is there anything special I should be doing to have access
to
> it?
It's only available in BioC devel and as a source package for now.
So if you are on Windows or Mac you need to use type="source" when
you do available.genomes() or biocLite(). For example on a Mac with
R 3.1.0:
> library(BSgenome)
> grep("GRCh38", available.genomes(), value=TRUE)
character(0)
> grep("GRCh38", available.genomes(type="source"), value=TRUE)
[1] "BSgenome.Hsapiens.NCBI.GRCh38"
Note that in BioC devel, there is a new utility, getBSgenome(),
documented in the same man page as available.genomes(), that is
the recommended way to lookup a BSgenome object by genome assembly
or by full BSgenome package name. If the BSgenome package is not
installed, it will tell you exactly how to install it:
> getBSgenome("GRCh38")
Error in .stopOnAvailablePkg(genome, is.source = TRUE) :
BSgenome.Hsapiens.NCBI.GRCh38 package is not currently installed.
You first need to install it, which you can do with:
library(BiocInstaller)
biocLite("BSgenome.Hsapiens.NCBI.GRCh38", type="source")
See ?getBSgenome for the details.
Cheers,
H.
>
> Thanks and best regards,
>
> - Hector
>
> Dr. Hector Zenil
> http://www.algorithmicnaturelab.org/hector.zenil
> Unit of Computational Medicine
> Karolinska Institute, Stockholm
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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